Revision: 20551
http://sourceforge.net/p/jmol/code/20551
Author: hansonr
Date: 2015-06-05 05:18:22 +0000 (Fri, 05 Jun 2015)
Log Message:
-----------
echo @{"cb="+cb} does not access function variable cb. There is some question
as to whether it should...
AtomSetCollection.java not clearing bsAtoms when a set is deleted
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
2015-06-05 05:06:35 UTC (rev 20550)
+++ trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
2015-06-05 05:18:22 UTC (rev 20551)
@@ -37,7 +37,7 @@
private String aabb;
private boolean readPRE;
// private boolean readPOST;
- private float fracA = Float.NaN;
+ private float fracB = Float.NaN;
private Map<String, float[]> compositions;
private boolean getComposition;
private String listKey, listKeyCase;
@@ -111,14 +111,22 @@
protected void initializeReader() throws Exception {
readPRE = checkFilterKey("PRE");
// readPOST = !checkFilterKey("NOPOST");
- String s = getFilter("CA=");
forcePacked = !checkFilterKey("NOPACK");
+
+ String s;
+
+ s = getFilter("CA=");
if (s != null)
- fracA = parseFloatStr(s.substring(1));
+ fracB = (1 - parseFloatStr(s.substring(1)));
+
+ s = getFilter("CB=");
+ if (s != null)
+ fracB = parseFloatStr(s.substring(1));
+
s = getFilter("LIST=");
listKey = (s == null ? "HF" : s);
listKeyCase = listKey;
- getComposition = !Float.isNaN(fracA);
+ getComposition = !Float.isNaN(fracB);
discardLinesUntilStartsWith("[");
//asc.setAtomSetName(title = line.trim());
aabb = line.substring(1, line.indexOf("]"));
@@ -143,7 +151,7 @@
private boolean readPrePost() throws Exception {
fileModelNumber++;
String titleMsg = "" + (modelNumber+1)
- + (getComposition ? "," + fileModelNumber + "," + fracA : "");
+ + (getComposition ? "," + fileModelNumber + ", Cb=" + fracB : "");
elementLabel = null;
if (readPRE) {
readStructure(titleMsg);
@@ -180,12 +188,17 @@
if (key.toUpperCase().startsWith(listKey)) {
listKey = key.toUpperCase();
listKeyCase = key;
- asc.setAtomSetName(aabb + " " + (getComposition ? fracA + " " : " ") +
key + "=" + val);
+ asc.setAtomSetName(aabb + " " + (getComposition ? fracB + " " : " ") +
key + "=" + val);
listVal = parseFloatStr(val);
}
+ if (key.equals("Ca")) {
+ float ca = parseFloatStr(val);
+ if (getComposition && Math.abs((1 - ca) - fracB) > 0.01f)
+ return false;
+ } else
if (key.equals("Cb")) {
float cb = parseFloatStr(strcb = val);
- if (getComposition && Math.abs(cb - fracA) > 0.01f)
+ if (getComposition && Math.abs(cb - fracB) > 0.01f)
return false;
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2015-06-05 05:06:35 UTC (rev 20550)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2015-06-05 05:18:22 UTC (rev 20551)
@@ -450,7 +450,10 @@
public void removeCurrentAtomSet() {
if (iSet < 0)
return;
- ac = atomSetAtomIndexes[iSet];
+ int ai = atomSetAtomIndexes[iSet];
+ if (bsAtoms != null)
+ bsAtoms.clearBits(ai, ac);
+ ac = ai;
atomSetAtomCounts[iSet] = 0;
iSet--;
atomSetCount--;
Modified: trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java 2015-06-05
05:06:35 UTC (rev 20550)
+++ trunk/Jmol/src/org/jmol/api/JmolScriptEvaluator.java 2015-06-05
05:18:22 UTC (rev 20551)
@@ -74,8 +74,6 @@
void deleteAtomsInVariables(BS bsDeleted);
- Map<String, SV> getContextVariables();
-
boolean evalParallel(ScriptContext context, ShapeManager shapeManager);
void runScript(String script) throws ScriptException;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-06-05 05:06:35 UTC
(rev 20550)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-06-05 05:18:22 UTC
(rev 20551)
@@ -802,6 +802,8 @@
ScriptEval e = (new ScriptEval()).setViewer(vwr);
try {
// disallow end-of-script message and JavaScript script queuing
+ e.thisContext = thisContext;
+ e.contextVariables = contextVariables;
e.pushContext(null, "evalExp");
e.allowJSThreads = false;
} catch (ScriptException e1) {
@@ -819,13 +821,11 @@
if (compileScript(null, "e_x_p_r_e_s_s_i_o_n = " + expr, false)) {
if (compileOnly)
return aatoken[0];
- contextVariables = vwr.getContextVariables();
setStatement(aatoken[0]);
return (asVariable ? parameterExpressionList(2, -1, false).get(0)
: parameterExpressionString(2, 0));
}
} else if (expr instanceof T[]) {
- contextVariables = vwr.getContextVariables();
BS bs = atomExpression((T[]) expr, 0, 0, true, false, true, false);
return (asVariable ? SV.newV(T.bitset, bs) : bs);
@@ -1368,12 +1368,7 @@
// ///////////////// Script context support //////////////////////
- @Override
- public Map<String, SV> getContextVariables() {
- return contextVariables;
- }
-
- @Override
+ @Override
public ScriptContext getThisContext() {
return thisContext;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-06-05 05:06:35 UTC (rev
20550)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-06-05 05:18:22 UTC (rev
20551)
@@ -8956,10 +8956,6 @@
atomExpression));
}
- public Map<String, SV> getContextVariables() {
- return (getScriptManager() == null ? null : eval.getContextVariables());
- }
-
public ScriptContext getScriptContext(String why) {
return (getScriptManager() == null ? null : eval.getScriptContext(why));
}
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